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Bioinformatics Vol. 19 Suppl. 1 2003
Pages i215-i221
© 2003 Oxford University Press

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments

Orla O’Sullivan 1, Mark Zehnder 3, Des Higgins 1, Philipp Bucher 3, Aurelien Grosdidier 3 and Cédric Notredame 2,3,*

1 Department of Biochemistry, University College, Cork, Ireland
2 Information Génétique et Structurale, CNRS UMR-1889, 31, Chemin Joseph Aiguier, 13402 Marseille, France
3 Swiss Institute of Bioinformatics, Chemin des Boveresse, 155, 1066 Epalinges, Switzerland

Received on January 6, 2003 ; accepted on February 10, 2003

Motivation: We describe APDB, a novel measure for evaluating the quality of a protein sequence alignment, given two or more PDB structures. This evaluation does not require a reference alignment or a structure superposition. APDB is designed to efficiently and objectively benchmark multiple sequence alignment methods.

Results: Using existing collections of reference multiple sequence alignments and existing alignment methods, we show that APDB gives results that are consistent with those obtained using conventional evaluations. We also show that APDB is suitable for evaluating sequence alignments that are structurally equivalent. We conclude that APDB provides an alternative to more conventional methods used for benchmarking sequence alignment packages.

Availability: APDB is implemented in C, its source code and its documentation are available for free on request from the authors.

Contact: cedric.notredame{at}europe.com

* To whom correspondence should be addressed.


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